Added in -v nowobble=1 for split_rmdups. This is the only non-whitespace... (198a93b9) · Commits · Chaos / chaos.juicer

AWS/scripts/dups.awk

+15 −0

Changes for AWS/scripts/dups.awk: 15 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -50,8 +50,14 @@ function optcheck(tile1,tile2,x1,x2,y1,y2) {
		# Executed once, before beginning the file read
		BEGIN {
		i=0;
		if (length(nowobble)==0) {
		wobble1=4;
		wobble2=4;
		}
		else {
		wobble1=0;
		wobble2=0;
		}
		# names of output files
		# the variable "name" can be set via the -v flag
		dupname=name"dups.txt";
		@@ -95,6 +101,10 @@ $1 != p1 \|\| $2 != p2 \|\| $4 != p4 \|\| $5 != p5 \|\| $6 != p6 \|\| $8 != p8 \|\| abs($3-p
		}
		else dups[k]++; #places a 1 at dups[k]
		}
		if (abs(pos1[j]-pos1[k])>wobble1) {
		#print "test", pos1[j], pos1[k]
		break
		}
		}
		}
		}
		@@ -173,6 +183,11 @@ END {
		dups[k]++;
		}
		}
		if (abs(pos1[j]-pos1[k])>wobble1) {
		#print "test", pos1[j], pos1[k]
		break

		}
		}
		}
		}

AWS/scripts/split_rmdups.awk

+11 −3

Changes for AWS/scripts/split_rmdups.awk: 11 added lines, 3 removed lines.
Original line number	Diff line number	Diff line
		@@ -26,7 +26,6 @@
		# Dedup script that submits deduping jobs after splitting at known
		# non-duplicates
		# Juicer version 1.5

		BEGIN{
		tot=0;
		name=0;
		@@ -36,7 +35,13 @@ BEGIN{
		if (tot >= 1000000) {
		if (p1 != $1 \|\| p2 != $2 \|\| p4 != $4 \|\| p5 != $5 \|\| p8 != $8) {
		sname=sprintf("%s_msplit%04d_", groupname, name);
		if (justexact) {
		sysstring = sprintf("bsub -W %s -o %s -q %s -J %s <<- EOF\nawk -v nowobble=1 -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\nEOF\n", queuetime, outfile, queue, sname, juicedir, dir, sname, dir, name, dir, name);
		}
		else {
		sysstring = sprintf("bsub -W %s -o %s -q %s -J %s <<- EOF\nawk -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\nEOF\n", queuetime, outfile, queue, sname, juicedir, dir, sname, dir, name, dir, name);
		}

		system(sysstring);
		if (name==0) {
		waitstring=sprintf("done(%s)", sname);
		@@ -55,7 +60,12 @@ BEGIN{
		}
		END {
		sname=sprintf("%s_msplit%04d_", groupname, name);
		if (justexact) {
		sysstring = sprintf("bsub -W %s -o %s -q %s -J %s <<-EOF\nawk -v nowobble=1 -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\nEOF\n", queuetime, outfile, queue, sname, juicedir, dir, sname, dir, name, dir, name);
		}
		else {
		sysstring = sprintf("bsub -W %s -o %s -q %s -J %s <<-EOF\nawk -f %s/scripts/dups.awk -v name=%s/%s %s/split%04d;\nEOF\n", queuetime, outfile, queue, sname, juicedir, dir, sname, dir, name, dir, name);
		}
		system(sysstring);
		if (name==0) {
		waitstring=sprintf("done(%s)", sname);
		@@ -67,6 +77,4 @@ END {
		system(sysstring);
		sysstring = sprintf("bsub -W %s -o %s -q %s -J %s_rmsplit -w \"done(%s_catsplit)\" <<- EOF\n rm %s/_msplit_optdups.txt; rm %s/_msplit_dups.txt; rm %s/_msplit_merged_nodups.txt; rm %s/split*;\nEOF",queuetime, outfile, queue, groupname, groupname, dir, dir, dir, dir);
		system(sysstring);


		}

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